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Weiqun Peng - One of the best experts on this subject based on the ideXlab platform.
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Interplay of BAF and MLL4 promotes cell type-specific enhancer activation.
Nature communications, 2021Co-Authors: Young-kwon Park, Ji-eun Lee, Kaitlin Mckernan, Tommy O'haren, Zhijiang Yan, Weidong Wang, Weiqun PengAbstract:Cell type-specific enhancers are activated by coordinated actions of lineage-determining transcription factors (LDTFs) and chromatin regulators. The SWI/SNF chromatin remodeling complex BAF and the histone H3K4 methyltransferase MLL4 (KMT2D) are both implicated in enhancer activation. However, the interplay between BAF and MLL4 in enhancer activation remains unclear. Using adipogenesis as a model system, we identify BAF as the major SWI/SNF complex that colocalizes with MLL4 and LDTFs on active enhancers and is required for cell differentiation. In contrast, the promoter enriched SWI/SNF complex PBAF is dispensable for adipogenesis. By depleting BAF subunits SMARCA4 (BRG1) and SMARCB1 (SNF5) as well as MLL4 in cells, we show that BAF and MLL4 reciprocally regulate each other's binding on active enhancers before and during adipogenesis. By focusing on enhancer activation by the adipogenic pioneer transcription factor C/EBPβ without inducing cell differentiation, we provide direct evidence for an interdependent relationship between BAF and MLL4 in activating cell type-specific enhancers. Together, these findings reveal a positive feedback between BAF and MLL4 in promoting LDTF-dependent activation of cell type-specific enhancers.
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MLL3/MLL4 methyltransferase activities regulate embryonic stem cell differentiation independent of enhancer H3K4me1
2020Co-Authors: Guojia Xie, Younghoon Jang, Chengyu Liu, Ji-eun Lee, Young-kwon Park, Kaitlin Mckernan, Weiqun PengAbstract:Enhancers drive cell-type-specific gene transcription and are marked by H3K4me1. MLL4 (KMT2D), a major H3K4me1 methyltransferase with partial functional redundancy with MLL3 (KMT2C), is critical for enhancer activation and cell-type-specific gene induction during cell differentiation and development. However, the roles of MLL3/4-mediated enhancer H3K4me1 and MLL3/4 enzymatic activities in general in these processes remain unclear. Here, we report that MLL3/4 enzymatic activities are partially redundant during mouse development. Simultaneous elimination of both leads to embryonic lethality around E8.5. Using embryoid body (EB) differentiation as an in vitro model for early embryonic development, we show that Mll3 knockout MLL4 enzyme-dead embryonic stem cells (ESCs) are capable of differentiating towards the three germ layers but display severe cavitation defects, likely due to impaired induction of visceral endoderm. Importantly, MLL3/4-catalyzed H3K4me1 is dispensable for enhancer activation during early EB differentiation and lineage-specific neural differentiation. Together, these results suggest a critical, but enhancer H3K4me1-independent, role of MLL3/4 enzymatic activities in early embryonic development and ESC differentiation. HighlightsO_LISimultaneous elimination of MLL3 and MLL4 enzymatic activities leads to early embryonic lethality in mice C_LIO_LIMLL3/4 enzymatic activities are dispensable for ESC differentiation towards the three germ layers C_LIO_LIESCs lacking MLL3/4 enzymatic activities show cavitation defects during EB differentiation, likely due to impaired VE induction C_LIO_LIMLL3/4-catalyzed H3K4me1 is dispensable for enhancer activation in ESC differentiation C_LI
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mll3 MLL4 methyltransferase activities regulate embryonic stem cell differentiation independent of enhancer h3k4me1
bioRxiv, 2020Co-Authors: Guojia Xie, Younghoon Jang, Chengyu Liu, Ji-eun Lee, Young-kwon Park, Kaitlin Mckernan, Weiqun PengAbstract:Enhancers drive cell-type-specific gene transcription and are marked by H3K4me1. MLL4 (KMT2D), a major H3K4me1 methyltransferase with partial functional redundancy with MLL3 (KMT2C), is critical for enhancer activation and cell-type-specific gene induction during cell differentiation and development. However, the roles of MLL3/4-mediated enhancer H3K4me1 and MLL3/4 enzymatic activities in general in these processes remain unclear. Here, we report that MLL3/4 enzymatic activities are partially redundant during mouse development. Simultaneous elimination of both leads to embryonic lethality around E8.5. Using embryoid body (EB) differentiation as an in vitro model for early embryonic development, we show that Mll3 knockout MLL4 enzyme-dead embryonic stem cells (ESCs) are capable of differentiating towards the three germ layers but display severe cavitation defects, likely due to impaired induction of visceral endoderm. Importantly, MLL3/4-catalyzed H3K4me1 is dispensable for enhancer activation during early EB differentiation and lineage-specific neural differentiation. Together, these results suggest a critical, but enhancer H3K4me1-independent, role of MLL3/4 enzymatic activities in early embryonic development and ESC differentiation. HighlightsO_LISimultaneous elimination of MLL3 and MLL4 enzymatic activities leads to early embryonic lethality in mice C_LIO_LIMLL3/4 enzymatic activities are dispensable for ESC differentiation towards the three germ layers C_LIO_LIESCs lacking MLL3/4 enzymatic activities show cavitation defects during EB differentiation, likely due to impaired VE induction C_LIO_LIMLL3/4-catalyzed H3K4me1 is dispensable for enhancer activation in ESC differentiation C_LI
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Interplay of BAF and MLL4 promotes cell type-specific enhancer activation
2020Co-Authors: Young-kwon Park, Ji-eun Lee, Kaitlin Mckernan, Tommy O'haren, Zhijiang Yan, Weidong Wang, Weiqun PengAbstract:Cell type-specific enhancers are activated by coordinated actions of lineage-determining transcription factors (LDTFs) and chromatin regulators. The SWI/SNF complex BAF and the histone H3K4 methyltransferase MLL4 (KMT2D) are both implicated in enhancer activation. However, the interplay between BAF and MLL4 in enhancer activation remains unclear. Using adipogenesis as a model system, we identified BAF as the major SWI/SNF complex that colocalizes with MLL4 and LDTFs on active enhancers and is required for cell differentiation. In contrast, the promoter enriched SWI/SNF complex PBAF is dispensable for adipogenesis. By depleting BAF subunits SMARCA4 (BRG1) and SMARCB1 (SNF5) as well as MLL4 in cells, we showed an reciprocal regulation between BAF and MLL4 on active enhancers before and during adipogenesis. By focusing on enhancer activation by the adipogenic transcription factor C/EBPβ without inducing cell differentiation, we provide direct evidence for an interdependent relationship between BAF and MLL4 in activating cell type-specific enhancers. Together, these findings reveal a positive feedback between BAF and MLL4 in promoting LDTF-dependent activation of cell type-specific enhancers.
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Brd4 binds to active enhancers to control cell identity gene induction in adipogenesis and myogenesis.
Nature communications, 2017Co-Authors: Ji-eun Lee, Keiko Ozato, Younghoon Jang, Anup Dey, Young-kwon Park, Sarah Park, Nicholas Waring, Binbin Lai, Weiqun PengAbstract:The epigenomic reader Brd4 is an important drug target for cancers. However, its role in cell differentiation and animal development remains largely unclear. Using two conditional knockout mouse strains and derived cells, we demonstrate that Brd4 controls cell identity gene induction and is essential for adipogenesis and myogenesis. Brd4 co-localizes with lineage-determining transcription factors (LDTFs) on active enhancers during differentiation. LDTFs coordinate with H3K4 mono-methyltransferases MLL3/MLL4 (KMT2C/KMT2D) and H3K27 acetyltransferases CBP/p300 to recruit Brd4 to enhancers activated during differentiation. Brd4 deletion prevents the enrichment of Mediator and RNA polymerase II transcription machinery, but not that of LDTFs, MLL3/MLL4-mediated H3K4me1, and CBP/p300-mediated H3K27ac, on enhancers. Consequently, Brd4 deletion prevents enhancer RNA production, cell identity gene induction and cell differentiation. Interestingly, Brd4 is dispensable for maintaining cell identity genes in differentiated cells. These findings identify Brd4 as an enhancer epigenomic reader that links active enhancers with cell identity gene induction in differentiation.
Ji-eun Lee - One of the best experts on this subject based on the ideXlab platform.
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Interplay of BAF and MLL4 promotes cell type-specific enhancer activation.
Nature communications, 2021Co-Authors: Young-kwon Park, Ji-eun Lee, Kaitlin Mckernan, Tommy O'haren, Zhijiang Yan, Weidong Wang, Weiqun PengAbstract:Cell type-specific enhancers are activated by coordinated actions of lineage-determining transcription factors (LDTFs) and chromatin regulators. The SWI/SNF chromatin remodeling complex BAF and the histone H3K4 methyltransferase MLL4 (KMT2D) are both implicated in enhancer activation. However, the interplay between BAF and MLL4 in enhancer activation remains unclear. Using adipogenesis as a model system, we identify BAF as the major SWI/SNF complex that colocalizes with MLL4 and LDTFs on active enhancers and is required for cell differentiation. In contrast, the promoter enriched SWI/SNF complex PBAF is dispensable for adipogenesis. By depleting BAF subunits SMARCA4 (BRG1) and SMARCB1 (SNF5) as well as MLL4 in cells, we show that BAF and MLL4 reciprocally regulate each other's binding on active enhancers before and during adipogenesis. By focusing on enhancer activation by the adipogenic pioneer transcription factor C/EBPβ without inducing cell differentiation, we provide direct evidence for an interdependent relationship between BAF and MLL4 in activating cell type-specific enhancers. Together, these findings reveal a positive feedback between BAF and MLL4 in promoting LDTF-dependent activation of cell type-specific enhancers.
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mll3 MLL4 methyltransferase activities regulate embryonic stem cell differentiation independent of enhancer h3k4me1
bioRxiv, 2020Co-Authors: Guojia Xie, Younghoon Jang, Chengyu Liu, Ji-eun Lee, Young-kwon Park, Kaitlin Mckernan, Weiqun PengAbstract:Enhancers drive cell-type-specific gene transcription and are marked by H3K4me1. MLL4 (KMT2D), a major H3K4me1 methyltransferase with partial functional redundancy with MLL3 (KMT2C), is critical for enhancer activation and cell-type-specific gene induction during cell differentiation and development. However, the roles of MLL3/4-mediated enhancer H3K4me1 and MLL3/4 enzymatic activities in general in these processes remain unclear. Here, we report that MLL3/4 enzymatic activities are partially redundant during mouse development. Simultaneous elimination of both leads to embryonic lethality around E8.5. Using embryoid body (EB) differentiation as an in vitro model for early embryonic development, we show that Mll3 knockout MLL4 enzyme-dead embryonic stem cells (ESCs) are capable of differentiating towards the three germ layers but display severe cavitation defects, likely due to impaired induction of visceral endoderm. Importantly, MLL3/4-catalyzed H3K4me1 is dispensable for enhancer activation during early EB differentiation and lineage-specific neural differentiation. Together, these results suggest a critical, but enhancer H3K4me1-independent, role of MLL3/4 enzymatic activities in early embryonic development and ESC differentiation. HighlightsO_LISimultaneous elimination of MLL3 and MLL4 enzymatic activities leads to early embryonic lethality in mice C_LIO_LIMLL3/4 enzymatic activities are dispensable for ESC differentiation towards the three germ layers C_LIO_LIESCs lacking MLL3/4 enzymatic activities show cavitation defects during EB differentiation, likely due to impaired VE induction C_LIO_LIMLL3/4-catalyzed H3K4me1 is dispensable for enhancer activation in ESC differentiation C_LI
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MLL3/MLL4 methyltransferase activities regulate embryonic stem cell differentiation independent of enhancer H3K4me1
2020Co-Authors: Guojia Xie, Younghoon Jang, Chengyu Liu, Ji-eun Lee, Young-kwon Park, Kaitlin Mckernan, Weiqun PengAbstract:Enhancers drive cell-type-specific gene transcription and are marked by H3K4me1. MLL4 (KMT2D), a major H3K4me1 methyltransferase with partial functional redundancy with MLL3 (KMT2C), is critical for enhancer activation and cell-type-specific gene induction during cell differentiation and development. However, the roles of MLL3/4-mediated enhancer H3K4me1 and MLL3/4 enzymatic activities in general in these processes remain unclear. Here, we report that MLL3/4 enzymatic activities are partially redundant during mouse development. Simultaneous elimination of both leads to embryonic lethality around E8.5. Using embryoid body (EB) differentiation as an in vitro model for early embryonic development, we show that Mll3 knockout MLL4 enzyme-dead embryonic stem cells (ESCs) are capable of differentiating towards the three germ layers but display severe cavitation defects, likely due to impaired induction of visceral endoderm. Importantly, MLL3/4-catalyzed H3K4me1 is dispensable for enhancer activation during early EB differentiation and lineage-specific neural differentiation. Together, these results suggest a critical, but enhancer H3K4me1-independent, role of MLL3/4 enzymatic activities in early embryonic development and ESC differentiation. HighlightsO_LISimultaneous elimination of MLL3 and MLL4 enzymatic activities leads to early embryonic lethality in mice C_LIO_LIMLL3/4 enzymatic activities are dispensable for ESC differentiation towards the three germ layers C_LIO_LIESCs lacking MLL3/4 enzymatic activities show cavitation defects during EB differentiation, likely due to impaired VE induction C_LIO_LIMLL3/4-catalyzed H3K4me1 is dispensable for enhancer activation in ESC differentiation C_LI
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MLL3/MLL4-Associated PAGR1 Regulates Adipogenesis by Controlling Induction of C/EBPβ and C/EBPδ.
Molecular and cellular biology, 2020Co-Authors: Ji-eun Lee, Young-wook Cho, Chu-xia DengAbstract:Transcription factors C/EBPβ and C/EBPδ are induced within hours after initiation of adipogenesis in culture. They directly promote the expression of master adipogenic transcription factors peroxisome proliferator-activated receptor γ (PPARγ) and C/EBPα and are required for adipogenesis in vivo However, the mechanism that controls the induction of C/EBPβ and C/EBPδ remains elusive. We previously showed that histone methyltransferases MLL3/MLL4 and associated PTIP are required for the induction of PPARγ and C/EBPα during adipogenesis. Here, we show MLL3/MLL4/PTIP-associated protein PAGR1 (also known as PA1) cooperates with phosphorylated CREB and ligand-activated glucocorticoid receptor to directly control the induction of C/EBPβ and C/EBPδ in the early phase of adipogenesis. Deletion of Pagr1 in white and brown preadipocytes prevents the induction of C/EBPβ and C/EBPδ and leads to severe defects in adipogenesis. Adipogenesis defects in PAGR1-deficient cells can be rescued by the ectopic expression of C/EBPβ or PPARγ. Finally, the deletion of Pagr1 in Myf5+ precursor cells impairs brown adipose tissue and muscle development. Thus, by controlling the induction of C/EBPβ and C/EBPδ, PAGR1 plays a critical role in adipogenesis.
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mll3 MLL4 associated pagr1 regulates adipogenesis by controlling induction of c ebpβ and c ebpδ
Molecular and Cellular Biology, 2020Co-Authors: Ji-eun Lee, Young-wook Cho, Chu-xia DengAbstract:Transcription factors C/EBPβ and C/EBPδ are induced within hours after initiation of adipogenesis in culture. They directly promote the expression of master adipogenic transcription factors peroxisome proliferator-activated receptor γ (PPARγ) and C/EBPα and are required for adipogenesis in vivo However, the mechanism that controls the induction of C/EBPβ and C/EBPδ remains elusive. We previously showed that histone methyltransferases MLL3/MLL4 and associated PTIP are required for the induction of PPARγ and C/EBPα during adipogenesis. Here, we show MLL3/MLL4/PTIP-associated protein PAGR1 (also known as PA1) cooperates with phosphorylated CREB and ligand-activated glucocorticoid receptor to directly control the induction of C/EBPβ and C/EBPδ in the early phase of adipogenesis. Deletion of Pagr1 in white and brown preadipocytes prevents the induction of C/EBPβ and C/EBPδ and leads to severe defects in adipogenesis. Adipogenesis defects in PAGR1-deficient cells can be rescued by the ectopic expression of C/EBPβ or PPARγ. Finally, the deletion of Pagr1 in Myf5+ precursor cells impairs brown adipose tissue and muscle development. Thus, by controlling the induction of C/EBPβ and C/EBPδ, PAGR1 plays a critical role in adipogenesis.
Ali Shilatifard - One of the best experts on this subject based on the ideXlab platform.
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UTX Mutations in Human Cancer
Cancer cell, 2019Co-Authors: Lu Wang, Ali ShilatifardAbstract:Ubiquitously transcribed tetratricopeptide repeat on chromosome X (UTX, encoded by KDM6A) is a histone demethylase that targets di- and tri-methylated histone H3 lysine 27 (H3K27). UTX function has been linked to homeotic gene expression, embryonic development, and cellular reprogramming. UTX and its protein interactors within the COMPASS family, including the MLL3 and MLL4 lysine methyltransferases, are frequently mutated in multiple human cancers; however, the molecular basis of how these mutations contribute to oncogenesis remains unclear. Here, we discuss catalytic-dependent and -independent functions of UTX and its partners MLL3 and MLL4 as part of the COMPASS family during development and in oncogenesis.
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Multiple Roles for the MLL/COMPASS Family in the Epigenetic Regulation of Gene Expression and in Cancer
Annual Review of Cancer Biology, 2017Co-Authors: Joshua J. Meeks, Ali ShilatifardAbstract:The mixed lineage leukemia (MLL) gene is involved in numerous chromosomal translocations that result in acute myeloid and acute lymphoid leukemias. The MLL protein belongs to a family of six methyltransferases in mammals that can methylate histone H3 on lysine 4 (H3K4). The methyltransferase activities of MLL and the other family members, SETD1A, SETD1B, MLL2, MLL3 and MLL4, depend on their participation within macromolecular complexes called COMPASS (complex of proteins associated with Set1). Functional diversity within the COMPASS family includes the propensity to mono-, di-, or trimethylate H3K4 and to regulate promoters or enhancers. Recent cancer genome sequencing and animal studies have identified MLL3 and MLL4 as cancer drivers in a wide variety of hematologic and solid tumors. MLL3 and MLL4 implement monomethylation of H3K4 at enhancer regions, whereas another enzyme in MLL3 and MLL4 COMPASS, UTX, which is also frequently mutated in multiple types of cancer, demethylates H3K27me3, a modification a...
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MLL3/MLL4/COMPASS Family on Epigenetic Regulation of Enhancer Function and Cancer.
Cold Spring Harbor perspectives in medicine, 2016Co-Authors: Christie C. Sze, Ali ShilatifardAbstract:During development, precise spatiotemporal patterns of gene expression are coordinately controlled by cis-regulatory modules known as enhancers. Their crucial role in development helped spur numerous studies aiming to elucidate the functional properties of enhancers within their physiological and disease contexts. In recent years, the role of enhancer malfunction in tissue-specific tumorigenesis is increasingly investigated. Here, we direct our focus to two primary players in enhancer regulation and their role in cancer pathogenesis: MLL3 and MLL4, members of the COMPASS family of histone H3 lysine 4 (H3K4) methyltransferases, and their complex-specific subunit UTX, a histone H3 lysine 27 (H3K27) demethylase. We review the most recent evidence on the underlying roles of MLL3/MLL4 and UTX in cancer and highlight key outstanding questions to help drive future research and contribute to our fundamental understanding of cancer and facilitate identification of therapeutic opportunities.
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mll3 MLL4 compass family on epigenetic regulation of enhancer function and cancer
Cold Spring Harbor Perspectives in Medicine, 2016Co-Authors: Christie C. Sze, Ali ShilatifardAbstract:During development, precise spatiotemporal patterns of gene expression are coordinately controlled by cis-regulatory modules known as enhancers. Their crucial role in development helped spur numerous studies aiming to elucidate the functional properties of enhancers within their physiological and disease contexts. In recent years, the role of enhancer malfunction in tissue-specific tumorigenesis is increasingly investigated. Here, we direct our focus to two primary players in enhancer regulation and their role in cancer pathogenesis: MLL3 and MLL4, members of the COMPASS family of histone H3 lysine 4 (H3K4) methyltransferases, and their complex-specific subunit UTX, a histone H3 lysine 27 (H3K27) demethylase. We review the most recent evidence on the underlying roles of MLL3/MLL4 and UTX in cancer and highlight key outstanding questions to help drive future research and contribute to our fundamental understanding of cancer and facilitate identification of therapeutic opportunities.
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Multiple Roles for the MLL/COMPASS Family in Cancer
2016Co-Authors: Joshua J. Meeks, Ali ShilatifardAbstract:The mixed lineage leukemia (MLL) gene is involved in numerous chromosomal translocations that result in acute myeloid and acute lymphoid leukemias. The MLL protein is one of a family of six methyltransferases in mammals that can methylate histone H3 on lysine 4 (H3K4). The methyltransferase activities of MLL and the other family members SETD1A, SETD1B, MLL2, MLL3 and MLL4 depend on their participation within macromolecular complexes called COMPASS (Complex of Proteins associated with Set1). Functional diversity within the COMPASS family includes the propensity to mono-, di- or trimethylate H3K4 and to regulate promoters or enhancers. Recent cancer genome sequencing studies and animal studies have identified MLL3 and MLL4/COMPASS as cancer drivers in a wide variety of hematologic and solid tumors. MLL3 and MLL4/COMPASS implement monomethylation of H3K4 at enhancer regions, while another enzyme in the same complexes, UTX demethylates H3K27me3, a modification associated with transcription repression by the P...
Younghoon Jang - One of the best experts on this subject based on the ideXlab platform.
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MLL3/MLL4 methyltransferase activities regulate embryonic stem cell differentiation independent of enhancer H3K4me1
2020Co-Authors: Guojia Xie, Younghoon Jang, Chengyu Liu, Ji-eun Lee, Young-kwon Park, Kaitlin Mckernan, Weiqun PengAbstract:Enhancers drive cell-type-specific gene transcription and are marked by H3K4me1. MLL4 (KMT2D), a major H3K4me1 methyltransferase with partial functional redundancy with MLL3 (KMT2C), is critical for enhancer activation and cell-type-specific gene induction during cell differentiation and development. However, the roles of MLL3/4-mediated enhancer H3K4me1 and MLL3/4 enzymatic activities in general in these processes remain unclear. Here, we report that MLL3/4 enzymatic activities are partially redundant during mouse development. Simultaneous elimination of both leads to embryonic lethality around E8.5. Using embryoid body (EB) differentiation as an in vitro model for early embryonic development, we show that Mll3 knockout MLL4 enzyme-dead embryonic stem cells (ESCs) are capable of differentiating towards the three germ layers but display severe cavitation defects, likely due to impaired induction of visceral endoderm. Importantly, MLL3/4-catalyzed H3K4me1 is dispensable for enhancer activation during early EB differentiation and lineage-specific neural differentiation. Together, these results suggest a critical, but enhancer H3K4me1-independent, role of MLL3/4 enzymatic activities in early embryonic development and ESC differentiation. HighlightsO_LISimultaneous elimination of MLL3 and MLL4 enzymatic activities leads to early embryonic lethality in mice C_LIO_LIMLL3/4 enzymatic activities are dispensable for ESC differentiation towards the three germ layers C_LIO_LIESCs lacking MLL3/4 enzymatic activities show cavitation defects during EB differentiation, likely due to impaired VE induction C_LIO_LIMLL3/4-catalyzed H3K4me1 is dispensable for enhancer activation in ESC differentiation C_LI
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mll3 MLL4 methyltransferase activities regulate embryonic stem cell differentiation independent of enhancer h3k4me1
bioRxiv, 2020Co-Authors: Guojia Xie, Younghoon Jang, Chengyu Liu, Ji-eun Lee, Young-kwon Park, Kaitlin Mckernan, Weiqun PengAbstract:Enhancers drive cell-type-specific gene transcription and are marked by H3K4me1. MLL4 (KMT2D), a major H3K4me1 methyltransferase with partial functional redundancy with MLL3 (KMT2C), is critical for enhancer activation and cell-type-specific gene induction during cell differentiation and development. However, the roles of MLL3/4-mediated enhancer H3K4me1 and MLL3/4 enzymatic activities in general in these processes remain unclear. Here, we report that MLL3/4 enzymatic activities are partially redundant during mouse development. Simultaneous elimination of both leads to embryonic lethality around E8.5. Using embryoid body (EB) differentiation as an in vitro model for early embryonic development, we show that Mll3 knockout MLL4 enzyme-dead embryonic stem cells (ESCs) are capable of differentiating towards the three germ layers but display severe cavitation defects, likely due to impaired induction of visceral endoderm. Importantly, MLL3/4-catalyzed H3K4me1 is dispensable for enhancer activation during early EB differentiation and lineage-specific neural differentiation. Together, these results suggest a critical, but enhancer H3K4me1-independent, role of MLL3/4 enzymatic activities in early embryonic development and ESC differentiation. HighlightsO_LISimultaneous elimination of MLL3 and MLL4 enzymatic activities leads to early embryonic lethality in mice C_LIO_LIMLL3/4 enzymatic activities are dispensable for ESC differentiation towards the three germ layers C_LIO_LIESCs lacking MLL3/4 enzymatic activities show cavitation defects during EB differentiation, likely due to impaired VE induction C_LIO_LIMLL3/4-catalyzed H3K4me1 is dispensable for enhancer activation in ESC differentiation C_LI
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Selective binding of the PHD6 finger of MLL4 to histone H4K16ac links MLL4 and MOF.
Nature communications, 2019Co-Authors: Yi Zhang, Younghoon Jang, Ji-eun Lee, Jae-woo Ahn, Michael R. Holden, Evan M. Cornett, Krzysztof Krajewski, Brianna J. Klein, Shu Ping WangAbstract:Histone methyltransferase MLL4 is centrally involved in transcriptional regulation and is often mutated in human diseases, including cancer and developmental disorders. MLL4 contains a catalytic SET domain that mono-methylates histone H3K4 and seven PHD fingers of unclear function. Here, we identify the PHD6 finger of MLL4 (MLL4-PHD6) as a selective reader of the epigenetic modification H4K16ac. The solution NMR structure of MLL4-PHD6 in complex with a H4K16ac peptide along with binding and mutational analyses reveal unique mechanistic features underlying recognition of H4K16ac. Genomic studies show that one third of MLL4 chromatin binding sites overlap with H4K16ac-enriched regions in vivo and that MLL4 occupancy in a set of genomic targets depends on the acetyltransferase activity of MOF, a H4K16ac-specific acetyltransferase. The recognition of H4K16ac is conserved in the PHD7 finger of paralogous MLL3. Together, our findings reveal a previously uncharacterized acetyllysine reader and suggest that selective targeting of H4K16ac by MLL4 provides a direct functional link between MLL4, MOF and H4K16 acetylation.
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h3 3k4m destabilizes enhancer h3k4 methyltransferases mll3 MLL4 and impairs adipose tissue development
Nucleic Acids Research, 2019Co-Authors: Younghoon Jang, Lenan Zhuang, Ji-eun Lee, Young-kwon Park, Aaron Broun, Chunxin Wang, Eugene Froimchuk, Cirong LiuAbstract:Histone 3 lysine 4 (H3K4) methyltransferases MLL3 and MLL4 (MLL3/4) are required for enhancer activation during cell differentiation, though the mechanism is incompletely understood. We have attempted to address this issue by generating two mouse lines: one expressing H3.3K4M, a lysine-4-to-methionine (K4M) mutation of histone H3.3 that inhibits H3K4 methylation, and the other carrying conditional double knockout of MLL3/4 enzymatic SET domain. Expression of H3.3K4M in lineage-specific precursor cells depletes H3K4 methylation and impairs adipose tissue and muscle development. Mechanistically, H3.3K4M prevents enhancer activation in adipogenesis by destabilizing MLL3/4 proteins but not other Set1-like H3K4 methyltransferases MLL1, MLL2, SET1A and SET1B. Notably, deletion of the enzymatic SET domain in lineage-specific precursor cells mimics H3.3K4M expression, destabilizes MLL3/4 proteins, and prevents adipose tissue and muscle development. Interestingly, destabilization of MLL3/4 by H3.3K4M in adipocytes does not affect adipose tissue maintenance and thermogenic function. Together, our findings indicate that expression of H3.3K4M, or deletion of the enzymatic SET domain, destabilizes enhancer H3K4 methyltransferases MLL3/4 and impairs adipose tissue and muscle development.
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H3.3K4M destabilizes enhancer H3K4 methyltransferases MLL3/MLL4 and impairs adipose tissue development.
Nucleic acids research, 2018Co-Authors: Younghoon Jang, Lenan Zhuang, Ji-eun Lee, Young-kwon Park, Aaron Broun, Chunxin Wang, Eugene Froimchuk, Cirong LiuAbstract:Histone 3 lysine 4 (H3K4) methyltransferases MLL3 and MLL4 (MLL3/4) are required for enhancer activation during cell differentiation, though the mechanism is incompletely understood. We have attempted to address this issue by generating two mouse lines: one expressing H3.3K4M, a lysine-4-to-methionine (K4M) mutation of histone H3.3 that inhibits H3K4 methylation, and the other carrying conditional double knockout of MLL3/4 enzymatic SET domain. Expression of H3.3K4M in lineage-specific precursor cells depletes H3K4 methylation and impairs adipose tissue and muscle development. Mechanistically, H3.3K4M prevents enhancer activation in adipogenesis by destabilizing MLL3/4 proteins but not other Set1-like H3K4 methyltransferases MLL1, MLL2, SET1A and SET1B. Notably, deletion of the enzymatic SET domain in lineage-specific precursor cells mimics H3.3K4M expression, destabilizes MLL3/4 proteins, and prevents adipose tissue and muscle development. Interestingly, destabilization of MLL3/4 by H3.3K4M in adipocytes does not affect adipose tissue maintenance and thermogenic function. Together, our findings indicate that expression of H3.3K4M, or deletion of the enzymatic SET domain, destabilizes enhancer H3K4 methyltransferases MLL3/4 and impairs adipose tissue and muscle development.
Michael S. Cosgrove - One of the best experts on this subject based on the ideXlab platform.
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Targeted Disruption of the Interaction between WD-40 Repeat Protein 5 (WDR5) and Mixed Lineage Leukemia (MLL)/SET1 Family Proteins Specifically Inhibits MLL1 and SETd1A Methyltransferase Complexes.
The Journal of biological chemistry, 2016Co-Authors: Nilda L. Alicea-velázquez, Stephen A. Shinsky, Daniel M. Loh, Jeong Heon Lee, David G. Skalnik, Michael S. CosgroveAbstract:Abstract MLL1 belongs to the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases, composed of MLL1–4 and SETd1A/B. MLL1 translocations are present in acute leukemias, and mutations in several family members are associated with cancer and developmental disorders. MLL1 associates with a subcomplex containing WDR5, RbBP5, ASH2L, and DPY-30 (WRAD), forming the MLL1 core complex required for H3K4 mono- and dimethylation and transcriptional activation. Core complex assembly requires interaction of WDR5 with the MLL1 Win (WDR5 interaction) motif, which is conserved across the SET1 family. Agents that mimic the SET1 family Win motif inhibit the MLL1 core complex and have become an attractive approach for targeting MLL1 in cancers. Like MLL1, other SET1 family members interact with WRAD, but the roles of the Win motif in complex assembly and enzymatic activity remain unexplored. Here, we show that the Win motif is necessary for interaction of WDR5 with all members of the human SET1 family. Mutation of the Win motif-WDR5 interface severely disrupts assembly and activity of MLL1 and SETd1A complexes but only modestly disrupts MLL2/4 and SETd1B complexes without significantly altering enzymatic activity in vitro. Notably, in the absence of WDR5, MLL3 interacts with RAD and shows enhanced activity. To further probe the role of the Win motif-WDR5 interaction, we designed a peptidomimetic that binds WDR5 (Kd ∼3 nm) and selectively inhibits activity of MLL1 and SETd1A core complexes within the SET1 family. Our results reveal that SET1 family complexes with the weakest Win motif-WDR5 interaction are more susceptible to Win motif-based inhibitors.
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Unique Role of the WD-40 Repeat Protein 5 (WDR5) Subunit within the Mixed Lineage Leukemia 3 (MLL3) Histone Methyltransferase Complex.
The Journal of biological chemistry, 2015Co-Authors: Stephen A. Shinsky, Michael S. CosgroveAbstract:The MLL3 (mixed lineage leukemia 3) protein is a member of the human SET1 family of histone H3 lysine 4 methyltransferases and contains the conserved WDR5 interaction (Win) motif and the catalytic suppressor of variegation, enhancer of zeste, trithorax (SET) domain. The human SET1 family includes MLL1-4 and SETd1A/B, which all interact with a conserved subcomplex containing WDR5, RbBP5, Ash2L, and DPY-30 (WRAD) to form the minimal core complex required for full methyltransferase activity. However, recent evidence suggests that the WDR5 subunit may not be utilized in an identical manner within all SET1 family core complexes. Although the roles of WDR5 within the MLL1 core complex have been extensively studied, not much is known about the roles of WDR5 in other SET1 family core complexes. In this investigation, we set out to characterize the roles of the WDR5 subunit in the MLL3 core complex. We found that unlike MLL1, the MLL3 SET domain assembles with the RbBP5/Ash2L heterodimer independently of the Win motif-WDR5 interaction. Furthermore, we observed that WDR5 inhibits the monomethylation activity of the MLL3 core complex, which is dependent on the Win motif. We also found evidence suggesting that the WRAD subcomplex catalyzes weak H3K4 monomethylation within the context of the MLL3 core complex. Furthermore, solution structures of the MLL3 core complex assembled with and without WDR5 by small angle x-ray scattering show similar overall topologies. Together, this work demonstrates a unique role for WDR5 in modulating the enzymatic activity of the MLL3 core complex.
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biochemical reconstitution and phylogenetic comparison of human set1 family core complexes involved in histone methylation
Journal of Biological Chemistry, 2015Co-Authors: Stephen A. Shinsky, Kelsey E Monteith, Susan Viggiano, Michael S. CosgroveAbstract:Mixed lineage leukemia protein-1 (MLL1) is a member of the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases that are required for metazoan development. MLL1 is the best characterized human SET1 family member, which includes MLL1-4 and SETd1A/B. MLL1 assembles with WDR5, RBBP5, ASH2L, DPY-30 (WRAD) to form the MLL1 core complex, which is required for H3K4 dimethylation and transcriptional activation. Because all SET1 family proteins interact with WRAD in vivo, it is hypothesized they are regulated by similar mechanisms. However, recent evidence suggests differences among family members that may reflect unique regulatory inputs in the cell. Missing is an understanding of the intrinsic enzymatic activities of different SET1 family complexes under standard conditions. In this investigation, we reconstituted each human SET1 family core complex and compared subunit assembly and enzymatic activities. We found that in the absence of WRAD, all but one SET domain catalyzes at least weak H3K4 monomethylation. In the presence of WRAD, all SET1 family members showed stimulated monomethyltransferase activity but differed in their di- and trimethylation activities. We found that these differences are correlated with evolutionary lineage, suggesting these enzyme complexes have evolved to accomplish unique tasks within metazoan genomes. To understand the structural basis for these differences, we employed a "phylogenetic scanning mutagenesis" assay and identified a cluster of amino acid substitutions that confer a WRAD-dependent gain-of-function dimethylation activity on complexes assembled with the MLL3 or Drosophila trithorax proteins. These results form the basis for understanding how WRAD differentially regulates SET1 family complexes in vivo.
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a non active site set domain surface crucial for the interaction of mll1 and the rbbp5 ash2l heterodimer within mll family core complexes
Journal of Molecular Biology, 2014Co-Authors: Stephen A. Shinsky, Valarie E. Vought, Michael J. Bamshad, Jay Shendure, Michael S. CosgroveAbstract:The mixed lineage leukemia-1 (MLL1) enzyme is a histone H3 lysine 4 (H3K4) monomethyltransferase and has served as a paradigm for understanding the mechanism of action of the human SET1 family of enzymes that include MLL1–MLL4 and SETd1a,b. Dimethylation of H3K4 requires a sub-complex including WRAD (WDR5, RbBP5, Ash2L, and DPY-30), which binds to each SET1 family member forming a minimal core complex that is required for multiple lysine methylation. We recently demonstrated that WRAD is a novel histone methyltransferase that preferentially catalyzes H3K4 dimethylation in a manner that is dependent on an unknown non-active-site surface from the MLL1 SET domain. Recent genome sequencing studies have identified a number of human disease-associated missense mutations that localize to the SET domains of several MLL family members. In this investigation, we mapped many of these mutations onto the three-dimensional structure of the SET domain and noticed that a subset of MLL2 (KMT2D, ALR, MLL4)-associated Kabuki syndrome missense mutations map to a common solvent-exposed surface that is not expected to alter enzymatic activity. We introduced these mutations into the MLL1 SET domain and observed that all are defective for H3K4 dimethylation by the MLL1 core complex, which is associated with a loss of the ability of MLL1 to interact with WRAD or with the RbBP5/Ash2L heterodimer. Our results suggest that amino acids from this surface, which we term the Kabuki interaction surface or KIS, are required for formation of a second active site within SET1 family core complexes.
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A Non-Active-Site SET Domain Surface Crucial for the Interaction of MLL1 and the RbBP5/Ash2L Heterodimer within MLL Family Core Complexes
Journal of molecular biology, 2014Co-Authors: Stephen A. Shinsky, Valarie E. Vought, Michael J. Bamshad, Jay Shendure, Michael S. CosgroveAbstract:The mixed lineage leukemia-1 (MLL1) enzyme is a histone H3 lysine 4 (H3K4) monomethyltransferase and has served as a paradigm for understanding the mechanism of action of the human SET1 family of enzymes that include MLL1–MLL4 and SETd1a,b. Dimethylation of H3K4 requires a sub-complex including WRAD (WDR5, RbBP5, Ash2L, and DPY-30), which binds to each SET1 family member forming a minimal core complex that is required for multiple lysine methylation. We recently demonstrated that WRAD is a novel histone methyltransferase that preferentially catalyzes H3K4 dimethylation in a manner that is dependent on an unknown non-active-site surface from the MLL1 SET domain. Recent genome sequencing studies have identified a number of human disease-associated missense mutations that localize to the SET domains of several MLL family members. In this investigation, we mapped many of these mutations onto the three-dimensional structure of the SET domain and noticed that a subset of MLL2 (KMT2D, ALR, MLL4)-associated Kabuki syndrome missense mutations map to a common solvent-exposed surface that is not expected to alter enzymatic activity. We introduced these mutations into the MLL1 SET domain and observed that all are defective for H3K4 dimethylation by the MLL1 core complex, which is associated with a loss of the ability of MLL1 to interact with WRAD or with the RbBP5/Ash2L heterodimer. Our results suggest that amino acids from this surface, which we term the Kabuki interaction surface or KIS, are required for formation of a second active site within SET1 family core complexes.